Association Analyses Discover and Validate Alleles for Stem Rust Resistance Using a Panel of U.S. Winter Wheat.

Stem rust has become a new threat to wheat production after the emergence and quick spread of race TTKSK. To evaluate the status of U.S. winter wheat resistance to stem rust, association mapping was conducted using a population of 137 accessions from five 2007-2008 winter wheat regional nurseries and 267 simple sequence repeat (SSR) markers including those previously reported markers for major stem rust resistance genes. Seedling reactions to six U.S. races (QFCS, QTHJ, RCRS, RKQQ, TPMK, TTTT) and TTKSK were evaluated in a greenhouse and adult plant resistance to bulked U.S. races were evaluated in the field at St. Paul, MN by USDA Cereal Disease Laboratory. A high proportion of accessions were resistant to QFCS and QTHJ in the seedling stage, but a low proportion of accessions were resistant to TTTT and TTKSK. Marker alleles XSr24#50-225 (Sr24) and Xscm9-241bp (Sr1A.1R) were associated with moderate resistance to all races at seedling and adult plants. Xwmc477-176 linked to Sr36 was associated with a high level of seedling resistance to TTKSK, QFCS, and QTHJ with infection type (IT) below ‘1-’ although only about 10% accessions carried the allele in the population. Marker Xventriup.Ln2 linked to Sr38/Lr37/Lr17 conferred a high level of seedling resistance to QFCS, QTHJ, RKQQ, and the bulked U.S. races at adult stage. Marker Xscm9-225 for Sr31 was associated with resistance to all US races but not TTKSK. Several new marker alleles were identified to be associated with unknown rust resistance genes. Marker Xgwm495-182 was associated with a high level of resistance to TTKSK; Xgwm484-185 showed the highest resistance to QFCS and TMPK; and markers Xgwm95-133, Xgwm313 -213, and Xgwm622-147 were associated with the highest resistance to QTHJ, RCRS, and TTTT. Introduction of new Sr genes and increasing the frequency of known resistance genes in US wheat breeding programs should facilitate genetic improvement wheat resistance to stem rust in U.S. wheat.